I have a similar setup, but with the 3100 which is similar, and I've noticed that whichever is the last to connect takes precedence. An example is that if I plug my iPhone into the deck right when it starts, it will begin playing. Then, about 15 seconds later after the BT autoconnects to the iPhone, the sound will cut out, but the ipod will continue playing. This is fixed by me simply disconnecting and re-connecting my phone via USB. I usually just wait about 20 seconds before connecting the usb.
I would suggest you try that. Hope that helps.